[2] | 1 | <tool id="gops_cluster_1" name="Cluster"> |
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| 2 | <description>the intervals of a query</description> |
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| 3 | <command interpreter="python">gops_cluster.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -d $distance -m $minregions -o $returntype</command> |
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| 4 | <inputs> |
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| 5 | <param format="interval" name="input1" type="data"> |
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| 6 | <label>Cluster intervals of</label> |
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| 7 | </param> |
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| 8 | <param name="distance" size="5" type="integer" value="1" help="(bp)"> |
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| 9 | <label>max distance between intervals</label> |
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| 10 | </param> |
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| 11 | <param name="minregions" size="5" type="integer" value="2"> |
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| 12 | <label>min number of intervals per cluster</label> |
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| 13 | </param> |
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| 14 | <param name="returntype" type="select" label="Return type"> |
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| 15 | <option value="1">Merge clusters into single intervals</option> |
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| 16 | <option value="2">Find cluster intervals; preserve comments and order</option> |
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| 17 | <option value="3">Find cluster intervals; output grouped by clusters</option> |
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| 18 | <option value="4">Find the smallest interval in each cluster</option> |
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| 19 | <option value="5">Find the largest interval in each cluster</option> |
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| 20 | </param> |
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| 21 | </inputs> |
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| 22 | <outputs> |
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| 23 | <data format="input" name="output" metadata_source="input1" /> |
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| 24 | </outputs> |
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| 25 | <code file="operation_filter.py"> |
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| 26 | <hook exec_after_process="exec_after_cluster" /> |
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| 27 | </code> |
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| 28 | <tests> |
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| 29 | <test> |
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| 30 | <param name="input1" value="5.bed" /> |
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| 31 | <param name="distance" value="1" /> |
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| 32 | <param name="minregions" value="2" /> |
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| 33 | <param name="returntype" value="1" /> |
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| 34 | <output name="output" file="gops-cluster-1.bed" /> |
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| 35 | </test> |
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| 36 | <test> |
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| 37 | <param name="input1" value="gops_cluster_bigint.bed" /> |
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| 38 | <param name="distance" value="1" /> |
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| 39 | <param name="minregions" value="2" /> |
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| 40 | <param name="returntype" value="1" /> |
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| 41 | <output name="output" file="gops-cluster-1.bed" /> |
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| 42 | </test> |
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| 43 | <test> |
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| 44 | <param name="input1" value="5.bed" /> |
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| 45 | <param name="distance" value="1" /> |
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| 46 | <param name="minregions" value="2" /> |
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| 47 | <param name="returntype" value="2" /> |
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| 48 | <output name="output" file="gops-cluster-2.bed" /> |
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| 49 | </test> |
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| 50 | <test> |
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| 51 | <param name="input1" value="5.bed" /> |
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| 52 | <param name="distance" value="1" /> |
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| 53 | <param name="minregions" value="2" /> |
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| 54 | <param name="returntype" value="3" /> |
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| 55 | <output name="output" file="gops-cluster-3.bed" /> |
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| 56 | </test> |
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| 57 | </tests> |
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| 58 | <help> |
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| 59 | |
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| 60 | .. class:: infomark |
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| 61 | |
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| 62 | **TIP:** If your query does not appear in the pulldown menu, it means that it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns. |
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| 63 | |
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| 64 | ----- |
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| 65 | |
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| 66 | **Screencasts!** |
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| 67 | |
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| 68 | See Galaxy Interval Operation Screencasts_ (right click to open this link in another window). |
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| 69 | |
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| 70 | .. _Screencasts: http://bitbucket.org/galaxy/galaxy-central/wiki/GopsDesc |
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| 71 | |
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| 72 | ----- |
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| 73 | |
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| 74 | **Syntax** |
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| 75 | |
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| 76 | - **Maximum distance** is greatest distance in base pairs allowed between intervals that will be considered "clustered". **Negative** values for distance are allowed, and are useful for clustering intervals that overlap. |
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| 77 | - **Minimum intervals per cluster** allow a threshold to be set on the minimum number of intervals to be considered a cluster. Any area with less than this minimum will not be included in the output. |
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| 78 | - **Merge clusters into single intervals** outputs intervals that span the entire cluster. |
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| 79 | - **Find cluster intervals; preserve comments and order** filters out non-cluster intervals while maintaining the original ordering and comments in the file. |
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| 80 | - **Find cluster intervals; output grouped by clusters** filters out non-cluster intervals, but outputs the cluster intervals so that they are grouped together. Comments and original ordering in the file are lost. |
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| 81 | |
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| 82 | ----- |
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| 83 | |
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| 84 | **Example** |
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| 85 | |
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| 86 | .. image:: ../static/operation_icons/gops_cluster.gif |
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| 87 | |
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| 88 | </help> |
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| 89 | </tool> |
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